Bioinformatics

A simple statistical test to infer the causality of target/phenotype correlation from small molecule phenotypic screens
pp. 301-305(5)
Authors: Wei, Xin; Hoffman, Ann F.; Hamilton, Shannon M.; Xiang, Qing; He, Yang; So, W. Venus; So, Sung-Sau; Mark, David

InFiRe a novel computational method for the identification of insertion sites in transposon mutagenized bacterial genomes
pp. 306-310(5)
Authors: Shevchuk, Olga; Roselius, Louisa; Gnther, Gabriele; Klein, Johannes; Jahn, Dieter; Steinert, Michael; Mnch, Richard

SomaticSniper: identification of somatic point mutations in whole genome sequencing data
pp. 311-317(7)
Authors: Larson, David E.; Harris, Christopher C.; Chen, Ken; Koboldt, Daniel C.; Abbott, Travis E.; Dooling, David J.; Ley, Timothy J.; Mardis, Elaine R.; Wilson, Richard K.; Ding, Li

Detection of microRNAs in color space
pp. 318-323(6)
Authors: Marco, Antonio; Griffiths-Jones, Sam

SCPC: a method to structurally compare protein complexes
pp. 324-330(7)
Authors: Koike, Ryotaro; Ota, Motonori

Prediction and analysis of nucleotide-binding residues using sequence and sequence-derived structural descriptors
pp. 331-341(11)
Authors: Chen, Ke; Mizianty, Marcin J.; Kurgan, Lukasz

HydroPaCe: understanding and predicting cross-inhibition in serine proteases through hydrophobic patch centroids
pp. 342-349(8)
Authors: Gonalves-Almeida, V. M.; Pires, D. E. V.; de Melo-Minardi, R. C.; da Silveira, C. H.; Meira, W.; Santoro, M. M.

Inhibition of HIV-1 protease: the rigidity perspective
pp. 350-357(8)
Authors: Heal, J. W.; Jimenez-Roldan, J. E.; Wells, S. A.; Freedman, R. B.; Rmer, R. A.

M³: an improved SNP calling algorithm for Illumina BeadArray data
pp. 358-365(8)
Authors: Li, Gengxin; Gelernter, Joel; Kranzler, Henry R.; Zhao, Hongyu

Gaussian process modelling for bicoid mRNA regulation in spatio-temporal Bicoid profile
pp. 366-372(7)
Authors: Liu, Wei; Niranjan, Mahesan

Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data
pp. 373-380(8)
Authors: Karnovsky, Alla; Weymouth, Terry; Hull, Tim; Tarcea, V. Glenn; Scardoni, Giovanni; Laudanna, Carlo; Sartor, Maureen A.; Stringer, Kathleen A.; Jagadish, H. V.; Burant, Charles; Athey, Brian; Omenn, Gilbert S.

Minimal cut sets in a metabolic network are elementary modes in a dual network
pp. 381-387(7)
Authors: Ballerstein, Kathrin; von Kamp, Axel; Klamt, Steffen; Haus, Utz-Uwe

Construction and completion of flux balance models from pathway databases
pp. 388-396(9)
Authors: Latendresse, Mario; Krummenacker, Markus; Trupp, Miles; Karp, Peter D.

Integrating human and murine anatomical gene expression data for improved comparisons
pp. 397-402(6)
Authors: Jimnez-Lozano, Natalia; Segura, Joan; Macas, Jos Ramn; Vega, Juanjo; Carazo, Jos Mara

SNPxGE²: a database for human SNPcoexpression associations
pp. 403-410(8)
Authors: Wang, Yupeng; Joseph, Sandeep J.; Liu, Xinyu; Kelley, Michael; Rekaya, Romdhane

The Virtual Fly Brain browser and query interface
pp. 411-415(5)
Authors: Milyaev, Nestor; Osumi-Sutherland, David; Reeve, Simon; Burton, Nicholas; Baldock, Richard A.; Armstrong, J. Douglas

PGAP: pan-genomes analysis pipeline
pp. 416-418(3)
Authors: Zhao, Yongbing; Wu, Jiayan; Yang, Junhui; Sun, Shixiang; Xiao, Jingfa; Yu, Jun

GenomeRunner: automating genome exploration
pp. 419-420(2)
Authors: Dozmorov, Mikhail G.; Cara, Lukas R.; Giles, Cory B.; Wren, Jonathan D.

Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools
pp. 421-422(2)
Authors: San Lucas, F. Anthony; Wang, Gao; Scheet, Paul; Peng, Bo

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data
pp. 423-425(3)
Authors: Boeva, Valentina; Popova, Tatiana; Bleakley, Kevin; Chiche, Pierre; Cappo, Julie; Schleiermacher, Gudrun; Janoueix-Lerosey, Isabelle; Delattre, Olivier; Barillot, Emmanuel

NRPSsp: non-ribosomal peptide synthase substrate predictor
pp. 426-427(2)
Authors: Prieto, Carlos; Garca-Estrada, Carlos; Lorenzana, Diego; Martn, Juan Francisco

B-SOLANA: an approach for the analysis of two-base encoding bisulfite sequencing data
pp. 428-429(2)
Authors: Kreck, Benjamin; Marnellos, George; Richter, Julia; Krueger, Felix; Siebert, Reiner; Franke, Andre

RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing
pp. 430-432(3)
Authors: Xi, Yuanxin; Bock, Christoph; Mller, Fabian; Sun, Deqiang; Meissner, Alexander; Li, Wei

Identification and removal of ribosomal RNA sequences from metatranscriptomes
pp. 433-435(3)
Authors: Schmieder, Robert; Lim, Yan Wei; Edwards, Robert

SitePainter: a tool for exploring biogeographical patterns
pp. 436-438(3)
Authors: Gonzalez, Antonio; Stombaugh, Jesse; Lauber, Christian L.; Fierer, Noah; Knight, Rob

DMAN: a Java tool for analysis of multi-well differential scanning fluorimetry experiments
pp. 439-440(2)
Authors: Wang, Conan K.; Weeratunga, Saroja K.; Pacheco, Chris M.; Hofmann, Andreas

MTBindingSim: simulate protein binding to microtubules
pp. 441-443(3)
Authors: Philip, Julia T.; Pence, Charles H.; Goodson, Holly V.

GWAtoolbox: an R package for fast quality control and handling of genome-wide association studies meta-analysis data
pp. 444-445(2)
Authors: Fuchsberger, Christian; Taliun, Daniel; Pramstaller, Peter P.; Pattaro, Cristian

PathVar: analysis of gene and protein expression variance in cellular pathways using microarray data
pp. 446-447(2)
Authors: Glaab, Enrico; Schneider, Reinhard

An infrastructure for ontology-based information systems in biomedicine: RICORDO case study
pp. 448-450(3)
Authors: Wimalaratne, Sarala M.; Grenon, Pierre; Hoehndorf, Robert; Gkoutos, Georgios V.; de Bono, Bernard

seeQTL: a searchable database for human eQTLs
pp. 451-452(2)
Authors: Xia, Kai; Shabalin, Andrey A.; Huang, Shunping; Madar, Vered; Zhou, Yi-Hui; Wang, Wei; Zou, Fei; Sun, Wei; Sullivan, Patrick F.; Wright, Fred A.